Examples:

In Simoun everyone is born female and upon turning seventeen go to a mystical spring where they choose to either remain female or become male. For those who choose to become male the process is a Slow Transformation. For example head mechanic Wapōrif went to the spring and became male two years before the series but still has the biggest bust in the series.

Happens to the snail people in Uzumaki, who develop a spiral pattern on their backs, then start developing other, more horrific traits over the course of several days.

In general, this seems to be a favorite trope for Junji Ito. Possibly the most horrific example occurs in a six page short titled "A Doll's Hellish Burial", in which a child contracts Early Onset Doll's Disease. She transforms first into something like a living doll, then into something that hopefully hasn't been a living anything for a long time.

The protagonist of The Santa Clause slowly changes to fit the part of Santa (gaining weight, becoming unable to shave).

The werewolves of the Ginger Snaps films transform slowly into wolflike creatures, over the course of days or weeks.

Seth's horrific transformation in The Fly (1986) starts out gradually with his fingernails becoming loose and his face having a subtle discoloration to it. Then his body parts begin falling off, starting with his ears, and the Body Horror climaxes with his decaying human skin being torn apart to reveal his true mutant fly form.

Wikus's transformation into a Prawn in District 9, to the point where by the very end, he's become one entirely.

In Lost in Space Dr Smith receives a spider bite — two decades later he's transformed into a huge spider creature.

Honeymoon: Bea's strange behavior and physical degradation over the course of her honeymoon is the result of being taken over by an alien puppeteer parasite. It gains more and more control over her mind and slowly transforms her into a host body. She's aware of the process the whole time and is unable to do anything about it.

Literature

People turning into donkeys in The Adventures of Pinocchio. In the original story, it took several days for the first part of the change (the ears) to occur.

When Tash is infected in Galaxy of Fear she starts off with a rash that, through that story, swells and spreads, sends off Tainted Veins, and she sweats and is unusually irritable. Then the rash starts oozing... then the ooze proves to be tendrils of the Blob Monster that she's turning into and moving about as the transformation speeds up. This is in a day or so.

Stock in trade of the Evilutionary Biologists in The Moreau Factor. Somewhat mitigated by the fact that their victims are mostly other scientists deliberately chosen because they would find the research opportunities presented by their transformations (if not the actual transformations themselves) intriguing.

In Seraphina Dragon's muscles are soft, and their wings incapable of flight for the first few minutes after transformation.

In Lord of the Rings, Gollum's transformation from hobbit to.... thing was centuries-long. It is implied that the Nazgul's transformation from humans to dark holes in reality was one, too.

In Warrior Wolf Women of the Wasteland, having sex causes the women of McDonaldland to start transforming into wolves. This happens anytime they have sex, and it is irreversible.

Dracula. Due to Dracula nightly visits to feed on Lucy, she becomes more weaker over time and describes that her senses have suddenly become more keener but she continues to have nightmares of dark beings. By the third visit, she's lost so much of her blood that her bite wounds eventually close up on their own, she gains fangs and her demeanor is uncharacteristically more seductive, signifying to Helsing it's too late to save her from becoming a vampire. Mina's transformation is slightly different due to Dracula feeding her his blood, cursing her to turn regardless if she stays alive or dies as long as he's alive. Indeed, she starts showing signs due to losing appetite for food, her canines slowly turning into fangs, sharing a psychic connection to Dracula and being unable to stay awake during the day but being much more lively at night.

Live-Action TV

The Outer Limits (1995): In the episode "Birthright", a U.S. Senator escapes from his security detail after his own men try to kill him, and gradually gets weird warts and such. It turns out that a race of reptiloid aliens had sent spies to study humans and the spies are turning back after the disguise wears off. The horror factor is the spies themselves didn't know they were aliens.

The Round the Twist episode "Nails" starts with a distressed boy showing the protagonist he now has three rows of nails, and telling her he's turning into a monster. By the end of the episode, he has become a merman.

The Halloween episode of That's So Raven has Raven and Chelsea slowly turning into cows over the course of the episode. While their physique is human, they get cow ears, tails, snouts, hooves, tongues, and also start eating and mooing like them. At the end of the episode they are completely transformed, but it is revealed that it was actually one of Raven's visions that she manages to prevent from happening.

In BIONICLE, after the Piraka bathe in mutagenic water for a short while, thanks to falling into a trap, they don't notice it, but they start developing aquatic capabilities. When we next meet them a couple of books later, we find that their whole bodies have diminished, reducing them to eel-like spines with their heads at the end.

Video Games

In Guild Wars Nightfall, Varesh transforms into a Margonite like appearence (and eventually a full margonite form) over the course of several missions. This involves getting 2 extra pairs of eyes (first appearing as bumbs, then fully appearing) and become a lot paler.

The Wanderer over several cutscenes in Diablo 2 gradually looks more and more evil, until in a final cutscene morphing fully into a Diablo form.

In Eternal Darkness one of the characters you play as is inflicted with a curse in their chapter, meaning he gradually rots and turns into an undead creature (this happens at set points in the level) while he tries to to warn Charlemagne before he meets the same fate. He fails and ends up trapped in a room in the church as an undead monster until another character finally puts him out of his misery in a boss battle a few hundred years later.

The Haunted Ruins: The general shopkeeper slowly transforms from a seemingly innocent girl into an evil witch the deeper you venture into the dungeon. At first it looks like she just put on makeup, but then she gets Pointy Ears, her cashier uniform becomes a skimpy dress, and a tiara and pointy nose begin to gradually form on her. This transformation is mostly amusing to watch because of how she keeps on insisting that her changing appearance is all in your head and how you simply MUST show the fabled "Dark Orb" to her as soon as you find it, mmkay?

The protagonist of Shadow of the Colossus gradually becomes battle-worn as he kills the Colossi. There is, eventually, an explanation for this.

In Skullgirls, this happens to Filia during her ending: Upon finding the Skull Heart, she wishes for Painwheel to return to normal, a seemingly pure wish that should be granted without problem by the Skull Heart note If the Skull Heart decides your wish is impure, you become the next Skullgirl. However, the Skull Heart finds that her motivations are not entirely selfless: Filia's wish is partially motivated by her desire to atone for her actions during her life as a member of Medici family. As a result, poor Filia is next in line for the title of Skullgirl, but since the wish was not entirely selfish, the transformation is not instant, allowing her to at least enjoy life with her childhood friend for a while.

A similar thing happens in Parasoul's ending. In order to save her sister, Umbrella, from becoming the next Skullgirl, she wishes that Umbrella will never become the Skullgirl. The Skull Heart grants the wish by Making Parasoul take her place. The transformation is slow enough for her to train Umbrella to defeat her when she finally turns.

Web Comics

In Exiern Dragons are born looking like humans and gradually transform into their true forms after they mature. The protagonist's sidekick/like interest (she can't admit to more than that) Denver is a larval dragon, though he doesn't know it. His sister was well along in her transformation when she was last seen.

In The Cartoon Man, Roy's initial transformation into a human cartoon character takes several days.

Whateley Universe: Some transformations from the Exemplar power have been said to take at least a year to fully complete.

Western Animation

The Alchemist's transformation into Skeleton King from Super Robot Monkey Team Hyperforce Go! falls under this category. Fortunately, it gave him just enough time to turn his pet monkeys into the Hyperforce. What wasn't shown until "Golden Age" though, was that he was slowly aging. These were his last chilling words as he became Skeleton King:

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